7AXZ

Ku70/80 complex apo form

Summary for 7AXZ

• Entry DOI: 10.2210/pdb7axz/pdb
• EMDB information: 11933
• Descriptor: X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 (2 entities in total)
• Functional Keywords: nhej, ku70/80, xrcc5, xrcc6, dna damage, dna binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 152757.48

Authors

Hnizda, A.,Tesina, P.,Novak, P.,Blundell, T.L. (deposition date: 2020-11-10, release date: 2021-02-10, Last modification date: 2024-05-01)

Primary citation

Hnizda, A.,Tesina, P.,Nguyen, T.B.,Kukacka, Z.,Kater, L.,Chaplin, A.K.,Beckmann, R.,Ascher, D.B.,Novak, P.,Blundell, T.L.
SAP domain forms a flexible part of DNA aperture in Ku70/80.
Febs J., 288:4382-4393, 2021

PubMed Abstract: Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double-strand DNA breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes DNA breaks and serves as an essential hub for recruitment of NHEJ components. Here, we describe intramolecular interactions of the Ku70 C-terminal domain, known as the SAP domain. Using single-particle cryo-electron microscopy, mass spectrometric analysis of intermolecular cross-linking and molecular modelling simulations, we captured variable positions of the SAP domain depending on DNA binding. The first position was localized at the DNA aperture in the Ku70/80 apo form but was not observed in the DNA-bound state. The second position, which was observed in both apo and DNA-bound states, was found below the DNA aperture, close to the helical arm of Ku70. The localization of the SAP domain in the DNA aperture suggests a function as a flexible entry gate for broken DNA. DATABASES: EM maps have been deposited in EMDB (EMD-11933). Coordinates have been deposited in Protein Data Bank (PDB 7AXZ). Other data are available from corresponding authors upon a request.

PubMed: 33511782
DOI: 10.1111/febs.15732

Experimental method

ELECTRON MICROSCOPY (3.2 Å)